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- PDB-1yci: Factor inhibiting HIF-1 alpha in complex with N-(carboxycarbonyl)... -

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Basic information

Entry
Database: PDB / ID: 1yci
TitleFactor inhibiting HIF-1 alpha in complex with N-(carboxycarbonyl)-D-phenylalanine
ComponentsHypoxia-inducible factor 1 alpha inhibitor
KeywordsTranscription regulator / oxidoreductase / FIH / HIF / DSBH / OXYGENASE / TRANSCRIPTION / HYPOXIA / INHIBITOR 2-OXOGLUTARATE / ASPARAGINYL HYDROXYLASE / HYDROXYLASE N-(CARBOXYCARBONYL)-D-PHENYLALANINE / NOFD / NDF
Function / homology
Function and homology information


hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / Notch binding ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / Notch binding / oxygen sensor activity / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / Jelly Rolls / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Helix Hairpins ...Clavaminate synthase-like / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Cupin-like domain 8 / Cupin-like domain / Jelly Rolls / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / N-(CARBOXYCARBONYL)-D-PHENYLALANINE / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH 1H2N / Resolution: 2.7 Å
AuthorsMcDonough, M.A. / Schofield, C.J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Selective inhibition of factor inhibiting hypoxia-inducible factor
Authors: McDonough, M.A. / McNeill, L.A. / Tilliet, M. / Papamicael, C.A. / Chen, Q.Y. / Banerji, B. / Hewitson, K.S. / Schofield, C.J.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 alpha
Authors: Elkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Seibel, J.F. / Schlemminger, I. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
History
DepositionDec 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypoxia-inducible factor 1 alpha inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1477
Polymers40,3281
Non-polymers8186
Water1,62190
1
A: Hypoxia-inducible factor 1 alpha inhibitor
hetero molecules

A: Hypoxia-inducible factor 1 alpha inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,29314
Polymers80,6572
Non-polymers1,63712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4520 Å2
ΔGint-130 kcal/mol
Surface area30070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.853, 86.853, 150.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hypoxia-inducible factor 1 alpha inhibitor / Hypoxia- inducible factor asparagine hydroxylase / Factor inhibiting HIF-1 / FIH-1


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN / Plasmid: PET28A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NDF / N-(CARBOXYCARBONYL)-D-PHENYLALANINE


Type: D-peptide linking / Mass: 237.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11NO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63 %
Description: Rejection criteria as rejection probability, REJECTION CRITERIA (PROBABILITY)) : 0.0001
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2M AMMONIUM SULPHATE, 4% PEG400, 0.1M HEPES PH7.5 ARGON ATMOSPHERE, 28MG/ML PROTEIN WITH 1MM FE(II), 10MM N-(CARBOXYCARBONYL)-D-PHENYLALANINE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488 / Wavelength: 1.488 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2004
RadiationMonochromator: double crystal Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.7→43.45 Å / Num. all: 16510 / Num. obs: 16510 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1619 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
RefinementMethod to determine structure: ISOMORPHOUS WITH 1H2N
Starting model: 1H2N

1h2n


Resolution: 2.7→43.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1589 10.1 %RANDOM
Rwork0.21 ---
obs0.21 15709 95.3 %-
all-15709 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.9107 Å2 / ksol: 0.352278 e/Å3
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.89 Å20 Å20 Å2
2---6.89 Å20 Å2
3---13.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.7→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 50 90 2855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.416 137 9.8 %
Rwork0.356 1263 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DOP.PARAMDOP.TOP

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